# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 18:52:28 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: [[(2~{R},3~{R},4~{S},5~{R})-5-[2-chloranyl-6-[(phenylmethyl)amino]purin-9-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](F)[C@@H](O[C@@H]1CO[P](O)(=O)C[P](O)(O)=O)n2cnc3c(NCc4ccccc4)nc(Cl)nc23
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 QCQ  QCQ  '[[(2~{R},3~{R},4~{S},5~{R})-5-[2-chloranyl-6-[(phenylmethyl)amino]purin-9-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid'  ligand  53  35  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QCQ
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 QCQ  O3'  O   OH1    0  -0.668  -17.5447  17.2623  -36.3656
 QCQ  C3'  C   CH1    0  -0.083  -16.8852  17.2935  -35.1243
 QCQ  C2'  C   CH1    0   0.158  -15.5468  17.9577  -35.3936
 QCQ  F04  F   F      0  -0.358  -14.6377  17.6201  -34.4073
 QCQ  C4'  C   CH1    0  -0.032  -17.5467  18.2563  -34.1220
 QCQ  C5'  C   CH2    0  -0.141  -17.4550  17.7793  -32.6881
 QCQ  O5'  O   O2     0  -0.630  -18.1454  18.6839  -31.8653
 QCQ  PA   P   P      0   1.252  -18.4740  18.2669  -30.2828
 QCQ  C3A  C   CH2    0  -1.016  -16.8567  18.2858  -29.4425
 QCQ  PB   P   P      0   1.191  -15.5552  19.5995  -29.7847
 QCQ  O1B  O   O      0  -0.846  -14.9185  19.1740  -31.1305
 QCQ  O2B  O   OP    -1  -0.898  -14.5843  19.4467  -28.6085
 QCQ  O3B  O   OP    -1  -0.892  -16.2651  20.9547  -29.8414
 QCQ  O1A  O   OP    -1  -0.814  -19.3586  19.3804  -29.7848
 QCQ  O2A  O   O      0  -0.828  -19.0182  16.8560  -30.2913
 QCQ  O4'  O   O2     0  -0.497  -16.8882  19.5163  -34.2853
 QCQ  C1'  C   CH1    0   0.175  -15.9131  19.4342  -35.2801
 QCQ  N9   N   NR5    0  -0.549  -14.7988  20.2764  -34.9385
 QCQ  C8   C   CR15   0   0.050  -14.1971  20.4302  -33.7123
 QCQ  N7   N   N      0  -0.477  -13.1405  21.1902  -33.7767
 QCQ  C5   C   CR56   0  -0.004  -13.0223  21.5461  -35.0981
 QCQ  C4   C   CR56   0   0.504  -14.0590  20.9859  -35.8332
 QCQ  N3   N   N      0  -0.435  -14.2803  21.1155  -37.1414
 QCQ  C2   C   CR6    0   0.275  -13.3709  21.8814  -37.6902
 QCQ  CL1  CL  CL     0  -0.116  -13.5603  22.1475  -39.3979
 QCQ  N1   N   N      0  -0.459  -12.3331  22.4759  -37.1505
 QCQ  C6   C   CR6    0   0.503  -12.1026  22.3245  -35.8329
 QCQ  N6   N   NH1    0  -0.626  -11.0079  22.9173  -35.3554
 QCQ  C29  C   CH2    0  -0.406  -10.5132  22.9016  -33.9948
 QCQ  C30  C   CR6    0   0.124  -10.7250  24.2203  -33.2938
 QCQ  C31  C   CR16   0  -0.307   -9.6520  25.0700  -33.0504
 QCQ  C32  C   CR16   0  -0.239   -9.8457  26.2934  -32.4198
 QCQ  C33  C   CR16   0  -0.264  -11.1200  26.6786  -32.0301
 QCQ  C34  C   CR16   0  -0.240  -12.1991  25.8353  -32.2713
 QCQ  C35  C   CR16   0  -0.288  -12.0020  24.6144  -32.8985
 QCQ  H1   H   HOH1   0   0.459  -18.4527  16.9736  -36.2282
 QCQ  H2   H   HCH1   0   0.261  -16.7598  16.2882  -34.7028
 QCQ  H3   H   HCH1   0   0.260  -15.1180  17.6996  -36.3629
 QCQ  H4   H   HCH1   0   0.242  -18.6050  18.3851  -34.3795
 QCQ  H5   H   HCH2   0   0.191  -17.9036  16.7791  -32.6481
 QCQ  H6   H   HCH2   0   0.211  -16.4083  17.6938  -32.3815
 QCQ  H7   H   HCH2   0   0.209  -17.1027  18.3283  -28.3746
 QCQ  H8   H   HCH2   0   0.205  -16.3826  17.3099  -29.5880
 QCQ  H12  H   HCH1   0   0.268  -16.2891  19.7798  -36.2505
 QCQ  H13  H   HCR5   0   0.347  -14.5808  19.9747  -32.7886
 QCQ  H14  H   HNH1   0   0.398  -10.4858  23.4622  -36.0259
 QCQ  H15  H   HCH2   0   0.286  -11.0013  22.0964  -33.4504
 QCQ  H16  H   HCH2   0   0.277   -9.4475  22.6690  -34.0272
 QCQ  H17  H   HCR6   0   0.252   -8.6547  24.7725  -33.3536
 QCQ  H18  H   HCR6   0   0.253   -9.0006  26.9440  -32.2348
 QCQ  H19  H   HCR6   0   0.254  -11.2738  27.6304  -31.5382
 QCQ  H20  H   HCR6   0   0.254  -13.1950  26.1287  -31.9648
 QCQ  H21  H   HCR6   0   0.255  -12.8456  23.9562  -33.0715

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 QCQ  CL1  C2   single    1.739  0.020  1.739
 QCQ  C2   N3   aromatic  1.310  0.020  1.310
 QCQ  C2   N1   aromatic  1.312  0.020  1.312
 QCQ  N3   C4   aromatic  1.333  0.020  1.333
 QCQ  N1   C6   aromatic  1.346  0.020  1.346
 QCQ  O3'  C3'  single    1.406  0.020  1.406
 QCQ  C4   C5   aromatic  1.389  0.020  1.389
 QCQ  C4   N9   aromatic  1.361  0.020  1.361
 QCQ  C6   N6   single    1.333  0.020  1.333
 QCQ  C6   C5   aromatic  1.411  0.020  1.411
 QCQ  C1'  C2'  single    1.526  0.020  1.526
 QCQ  C1'  N9   single    1.438  0.020  1.438
 QCQ  C1'  O4'  single    1.395  0.020  1.395
 QCQ  C2'  C3'  single    1.518  0.020  1.518
 QCQ  C2'  F04  single    1.383  0.020  1.383
 QCQ  N6   C29  single    1.448  0.020  1.448
 QCQ  C3'  C4'  single    1.539  0.020  1.539
 QCQ  C5   N7   aromatic  1.374  0.020  1.374
 QCQ  N9   C8   aromatic  1.374  0.020  1.374
 QCQ  O4'  C4'  single    1.431  0.020  1.431
 QCQ  C4'  C5'  single    1.514  0.020  1.514
 QCQ  C29  C30  single    1.508  0.020  1.508
 QCQ  C8   N7   aromatic  1.303  0.020  1.303
 QCQ  C31  C30  aromatic  1.390  0.020  1.390
 QCQ  C31  C32  aromatic  1.390  0.020  1.390
 QCQ  C30  C35  aromatic  1.394  0.020  1.394
 QCQ  C32  C33  aromatic  1.387  0.020  1.387
 QCQ  C35  C34  aromatic  1.387  0.020  1.387
 QCQ  C33  C34  aromatic  1.391  0.020  1.391
 QCQ  C5'  O5'  single    1.404  0.020  1.404
 QCQ  O5'  PA   single    1.669  0.020  1.669
 QCQ  O2A  PA   deloc     1.512  0.020  1.512
 QCQ  PA   O1A  deloc     1.507  0.020  1.507
 QCQ  PA   C3A  single    1.823  0.020  1.823
 QCQ  O1B  PB   deloc     1.548  0.020  1.548
 QCQ  C3A  PB   single    1.881  0.020  1.881
 QCQ  PB   O3B  deloc     1.531  0.020  1.531
 QCQ  PB   O2B  deloc     1.533  0.020  1.533
 QCQ  O3'  H1   single    0.850  0.020  0.980
 QCQ  C3'  H2   single    0.970  0.020  1.090
 QCQ  C2'  H3   single    0.970  0.020  1.090
 QCQ  C4'  H4   single    0.970  0.020  1.090
 QCQ  C5'  H5   single    0.970  0.020  1.090
 QCQ  C5'  H6   single    0.970  0.020  1.090
 QCQ  C3A  H7   single    0.970  0.020  1.090
 QCQ  C3A  H8   single    0.970  0.020  1.090
 QCQ  C1'  H12  single    0.970  0.020  1.090
 QCQ  C8   H13  single    0.930  0.020  1.080
 QCQ  N6   H14  single    0.860  0.020  1.020
 QCQ  C29  H15  single    0.970  0.020  1.090
 QCQ  C29  H16  single    0.970  0.020  1.090
 QCQ  C31  H17  single    0.930  0.020  1.080
 QCQ  C32  H18  single    0.930  0.020  1.080
 QCQ  C33  H19  single    0.930  0.020  1.080
 QCQ  C34  H20  single    0.930  0.020  1.080
 QCQ  C35  H21  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 QCQ  H1   O3'  C3'  108.85  3.000
 QCQ  H2   C3'  C4'  111.85  3.000
 QCQ  H2   C3'  C2'  111.61  3.000
 QCQ  C4'  C3'  C2'  102.75  3.000
 QCQ  H2   C3'  O3'  111.86  3.000
 QCQ  C4'  C3'  O3'  112.78  3.000
 QCQ  C2'  C3'  O3'  105.46  3.000
 QCQ  H3   C2'  C1'  112.92  3.000
 QCQ  H3   C2'  F04  108.52  3.000
 QCQ  C1'  C2'  F04  109.93  3.000
 QCQ  H3   C2'  C3'  113.62  3.000
 QCQ  F04  C2'  C3'  110.25  3.000
 QCQ  C1'  C2'  C3'  101.45  3.000
 QCQ  H4   C4'  O4'  108.29  3.000
 QCQ  H4   C4'  C5'  108.53  3.000
 QCQ  O4'  C4'  C5'  110.96  3.000
 QCQ  H4   C4'  C3'  109.59  3.000
 QCQ  C5'  C4'  C3'  113.18  3.000
 QCQ  O4'  C4'  C3'  106.18  3.000
 QCQ  H6   C5'  H5   108.05  3.000
 QCQ  H6   C5'  O5'  110.88  3.000
 QCQ  H5   C5'  O5'  111.41  3.000
 QCQ  H6   C5'  C4'  110.36  3.000
 QCQ  H5   C5'  C4'  107.28  3.000
 QCQ  O5'  C5'  C4'  108.80  3.000
 QCQ  PA   O5'  C5'  119.43  3.000
 QCQ  O2A  PA   O1A  118.69  3.000
 QCQ  O1A  PA   C3A  111.16  3.000
 QCQ  O2A  PA   C3A  109.37  3.000
 QCQ  C3A  PA   O5'  105.06  3.000
 QCQ  O1A  PA   O5'  104.14  3.000
 QCQ  O2A  PA   O5'  107.38  3.000
 QCQ  H8   C3A  H7   105.14  3.000
 QCQ  H8   C3A  PB   107.39  3.000
 QCQ  H7   C3A  PB   107.78  3.000
 QCQ  H8   C3A  PA   108.29  3.000
 QCQ  H7   C3A  PA   104.49  3.000
 QCQ  PB   C3A  PA   122.51  3.000
 QCQ  O3B  PB   O2B  114.23  3.000
 QCQ  O2B  PB   O1B  112.28  3.000
 QCQ  O3B  PB   O1B  113.69  3.000
 QCQ  O2B  PB   C3A  103.25  3.000
 QCQ  O3B  PB   C3A  107.71  3.000
 QCQ  O1B  PB   C3A  104.52  3.000
 QCQ  C1'  O4'  C4'  110.55  3.000
 QCQ  H12  C1'  N9   106.94  3.000
 QCQ  H12  C1'  O4'  111.89  3.000
 QCQ  N9   C1'  O4'  109.74  3.000
 QCQ  H12  C1'  C2'  108.75  3.000
 QCQ  O4'  C1'  C2'  106.13  3.000
 QCQ  N9   C1'  C2'  113.48  3.000
 QCQ  C4   N9   C8   106.88  3.000
 QCQ  C8   N9   C1'  128.07  3.000
 QCQ  C4   N9   C1'  124.79  3.000
 QCQ  H13  C8   N7   124.49  3.000
 QCQ  H13  C8   N9   123.41  3.000
 QCQ  N7   C8   N9   112.09  3.000
 QCQ  C5   N7   C8   105.57  3.000
 QCQ  C6   C5   C4   115.68  3.000
 QCQ  C6   C5   N7   134.42  3.000
 QCQ  C4   C5   N7   109.90  3.000
 QCQ  N3   C4   C5   127.16  3.000
 QCQ  C5   C4   N9   105.55  3.000
 QCQ  N3   C4   N9   127.28  3.000
 QCQ  C2   N3   C4   110.66  3.000
 QCQ  N1   C2   CL1  114.89  3.000
 QCQ  N1   C2   N3   129.93  3.000
 QCQ  CL1  C2   N3   115.18  3.000
 QCQ  C6   N1   C2   119.15  3.000
 QCQ  N6   C6   N1   116.17  3.000
 QCQ  N6   C6   C5   126.43  3.000
 QCQ  N1   C6   C5   117.39  3.000
 QCQ  H14  N6   C29  116.96  3.000
 QCQ  H14  N6   C6   115.26  3.000
 QCQ  C29  N6   C6   127.75  3.000
 QCQ  H16  C29  H15  107.18  3.000
 QCQ  H16  C29  C30  109.71  3.000
 QCQ  H15  C29  C30  110.59  3.000
 QCQ  H16  C29  N6   107.94  3.000
 QCQ  H15  C29  N6   108.97  3.000
 QCQ  C30  C29  N6   112.29  3.000
 QCQ  C35  C30  C31  118.99  3.000
 QCQ  C35  C30  C29  120.51  3.000
 QCQ  C31  C30  C29  120.49  3.000
 QCQ  H17  C31  C32  119.78  3.000
 QCQ  H17  C31  C30  119.57  3.000
 QCQ  C32  C31  C30  120.65  3.000
 QCQ  H18  C32  C33  120.15  3.000
 QCQ  H18  C32  C31  119.85  3.000
 QCQ  C33  C32  C31  120.00  3.000
 QCQ  H19  C33  C34  120.12  3.000
 QCQ  H19  C33  C32  120.16  3.000
 QCQ  C34  C33  C32  119.72  3.000
 QCQ  H20  C34  C35  119.83  3.000
 QCQ  H20  C34  C33  120.03  3.000
 QCQ  C35  C34  C33  120.13  3.000
 QCQ  H21  C35  C34  119.75  3.000
 QCQ  H21  C35  C30  119.75  3.000
 QCQ  C34  C35  C30  120.50  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 QCQ  CONST_01  C2   N3   C4   N9    180.00   0.0  0
 QCQ  CONST_02  C6   C5   C4   N9    180.00   0.0  0
 QCQ  CONST_03  N7   C5   C4   N9      0.00   0.0  0
 QCQ  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 QCQ  CONST_05  N3   C4   N9   C8    180.00   0.0  0
 QCQ  CONST_06  C5   C4   N9   C8      0.00   0.0  0
 QCQ  CONST_07  C4   C5   N7   C8      0.00   0.0  0
 QCQ  CONST_08  C6   C5   N7   C8    180.00   0.0  0
 QCQ  CONST_09  N3   C4   C5   N7    180.00   0.0  0
 QCQ  CONST_10  N1   C6   C5   N7    180.00   0.0  0
 QCQ  CONST_11  C4   N9   C8   N7      0.00   0.0  0
 QCQ  CONST_12  C2   N3   C4   C5      0.00   0.0  0
 QCQ  CONST_13  C2   N1   C6   C5      0.00   0.0  0
 QCQ  CONST_14  N1   C2   N3   C4      0.00   0.0  0
 QCQ  CONST_15  N1   C6   C5   C4      0.00   0.0  0
 QCQ  CONST_16  C6   N1   C2   N3      0.00   0.0  0
 QCQ  CONST_17  C6   C5   C4   N3      0.00   0.0  0
 QCQ  CONST_18  C33  C32  C31  C30     0.00   0.0  0
 QCQ  CONST_19  C33  C34  C35  C30     0.00   0.0  0
 QCQ  CONST_20  C34  C35  C30  C31     0.00   0.0  0
 QCQ  CONST_21  C34  C33  C32  C31     0.00   0.0  0
 QCQ  CONST_22  C35  C30  C31  C32     0.00   0.0  0
 QCQ  CONST_23  C35  C34  C33  C32     0.00   0.0  0
 QCQ  CONST_24  N3   C4   N9   C1'     0.00   0.0  0
 QCQ  CONST_25  C5   C4   N9   C1'   180.00   0.0  0
 QCQ  CONST_26  N7   C8   N9   C1'   180.00   0.0  0
 QCQ  CONST_27  N6   C6   C5   N7      0.00   0.0  0
 QCQ  CONST_28  CL1  C2   N3   C4    180.00   0.0  0
 QCQ  CONST_29  N6   C6   C5   C4    180.00   0.0  0
 QCQ  CONST_30  N6   C6   N1   C2    180.00   0.0  0
 QCQ  CONST_31  C6   N1   C2   CL1   180.00   0.0  0
 QCQ  CONST_32  C32  C31  C30  C29   180.00   0.0  0
 QCQ  CONST_33  C34  C35  C30  C29   180.00   0.0  0
 QCQ  CONST_34  H13  C8   N9   C1'     0.00   0.0  0
 QCQ  CONST_35  H18  C32  C31  C30   180.00   0.0  0
 QCQ  CONST_36  H20  C34  C35  C30   180.00   0.0  0
 QCQ  CONST_37  H21  C35  C30  C31   180.00   0.0  0
 QCQ  CONST_38  H19  C33  C32  C31   180.00   0.0  0
 QCQ  CONST_39  H17  C31  C32  C33   180.00   0.0  0
 QCQ  CONST_40  C29  N6   C6   C5      0.00   0.0  0
 QCQ  CONST_41  C29  N6   C6   N1    180.00   0.0  0
 QCQ  CONST_42  H14  N6   C6   C5    180.00   0.0  0
 QCQ  Var_01    C30  C29  N6   C6   -106.49  30.0  3
 QCQ  Var_02    C31  C30  C29  N6   -106.71  30.0  2
 QCQ  Var_03    O2A  PA   O5'  C5'   -46.32  30.0  3
 QCQ  Var_04    PB   C3A  PA   O5'    40.10  30.0  3
 QCQ  Var_05    O1B  PB   C3A  PA    -77.73  30.0  3
 QCQ  Var_06    H5   C5'  O5'  PA     49.91  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 QCQ  chir_01  C3'  O3'  C2'  C4'  negativ
 QCQ  chir_02  C2'  F04  C1'  C3'  positiv
 QCQ  chir_03  C4'  O4'  C3'  C5'  negativ
 QCQ  chir_05  C1'  C2'  N9   O4'  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 QCQ  plan-1  C29  0.020
 QCQ  plan-1  C30  0.020
 QCQ  plan-1  C31  0.020
 QCQ  plan-1  C32  0.020
 QCQ  plan-1  C33  0.020
 QCQ  plan-1  C34  0.020
 QCQ  plan-1  C35  0.020
 QCQ  plan-1  H17  0.020
 QCQ  plan-1  H18  0.020
 QCQ  plan-1  H19  0.020
 QCQ  plan-1  H20  0.020
 QCQ  plan-1  H21  0.020
 QCQ  plan-2  C1'  0.020
 QCQ  plan-2  N9   0.020
 QCQ  plan-2  C8   0.020
 QCQ  plan-2  N7   0.020
 QCQ  plan-2  C5   0.020
 QCQ  plan-2  C4   0.020
 QCQ  plan-2  N3   0.020
 QCQ  plan-2  C2   0.020
 QCQ  plan-2  CL1  0.020
 QCQ  plan-2  N1   0.020
 QCQ  plan-2  C6   0.020
 QCQ  plan-2  N6   0.020
 QCQ  plan-2  H13  0.020
 QCQ  plan-3  C6   0.020
 QCQ  plan-3  N6   0.020
 QCQ  plan-3  C29  0.020
 QCQ  plan-3  H14  0.020

